[3] Following the draft, he made his professional debut as a member of the Gulf Coast League Tigers.

Cornejo started 16 games for Jacksonville, posting a 5–7 record and an earned run average of 4.61.

In a preview of that game, the Seattle Post-Intelligencer compared him to future All-Star Matt Clement.

He had the lowest strikeout rate of any starting pitcher in over 20 years, striking out just 46 batters in 194.2 innings.

He was signed by the Chicago White Sox to a minor league contract in April 2006.